Biochemical Pathways Workbench

生化途径工作台

• 批准号: 0641037
• 负责人: Shankar Subramaniam
• 金额: $ 62.95万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-12-01 至 2011-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0641037&HistoricalAwards=false
• 关键词: Biochemical; Pathways; Workbench

The University of California-San Diego is awarded a grant to develop a comprehensive pathways database, query/analysis toolkit, interface infrastructure, and an authoring toolkit, called Biochemical Pathways Workbench (BPW) for biological networks. The goal of this Workbench is to provide scientists with a computational sandbox in which they can develop complex applications, or choose from an extensive set of analysis tools provided by the database. The project targets fundamental contributions in biological modeling, algorithm design, analytical modeling, statistical validation, and deployment into the existing Biology Workbench (http://workbench.sdsc.edu). The project will be a collaborative effort with Purdue University.Traditional data repositories provide interfaces to sequence and structure-based annotations. Given the emerging trend in biology towards pathways, networks, and systems, there is a need to provide data, analysis, and modeling interfaces to pathways. We will provide such an interface to various data sources from biochemical pathways and enhance these with data and applications from our own laboratory. The tool will offer interoperability with other data sources including sequence and expression databases, support an API using which programmers will be able to transparently query remote databases, and provide a graphical interface to its analysis tools in the form of an authoring toolkit. Using this toolkit, scientists will be able to experiment with diverse data sources integrated into BPW networks and databases. The infrastructure in an open architecture will be integrated into the Biochemical Pathways WorkBench, and made available to the broader science and education community. The project will invest considerable effort during the second year to develop instructional media courses at UCSD and Purdue that demonstrate the educational value of the tool.

加州大学迭戈大学获得了一项赠款，以开发全面的途径数据库，查询/分析工具包，界面基础架构和一个为生物网络的工具包，称为生化途径Workbench（BPW）。该工作台的目的是为科学家提供一个计算机沙箱，在该沙箱中可以开发复杂的应用程序，或者从数据库提供的大量分析工具中进行选择。该项目针对生物建模，算法设计，分析建模，统计验证和部署在现有生物学工作台（http://workbench.sdsc.edu）中的基本贡献。该项目将是与普渡大学的合作努力。传统数据存储库为序列和基于结构的注释提供了接口。鉴于生物学对途径，网络和系统的新兴趋势，需要提供数据，分析和建模界面到途径。我们将向来自生化途径的各种数据源提供这样的接口，并通过我们自己的实验室的数据和应用来增强这些界面。该工具将提供与其他数据源（包括序列和表达数据库）的互操作性，支持程序员将能够透明地查询远程数据库的API，并以创作工具包的形式为其分析工具提供图形接口。使用此工具包，科学家将能够尝试集成到BPW网络和数据库中的各种数据源。开放建筑中的基础设施将集成到生化途径工作台中，并提供给更广泛的科学和教育社区。该项目将在第二年投入大量努力，以在UCSD和Purdue开发教学媒体课程，以证明该工具的教育价值。